SMTL ID : 7drx.1

Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in 90PS with beryllium fluoride (E2P state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 11 residues within 4Å: Chain A: Y.585 Chain B: F.152, K.154, N.236, S.237, N.240, Y.288, K.291, H.347, W.348, P.349 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: G.440, D.667, K.668, T.669, G.990, K.1110, N.1133 Ligands: BEF.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.667, A:D.667

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 10 residues within 4Å: Chain A: K.436, D.439, D.667, T.669, T.671, D.1130, G.1131, N.1133, D.1134 Ligands: MG.2 No protein-ligand interaction detected (PLIP)

2 x 6PL: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

6PL.4: 12 residues within 4Å: Chain A: I.253, I.256, K.257, I.260, R.264, T.626, A.629, A.630, Y.633, P.649, W.652 Chain B: R.51 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.253, A:I.253, A:I.256, A:K.257, A:I.260, A:I.260, A:T.626, A:A.630, A:Y.633, A:W.652, A:W.652 Hydrogen bonds: A:R.264 6PL.5: 17 residues within 4Å: Chain A: P.246, V.249, I.253, Q.610, I.615, S.616, I.619, I.623, M.1222, M.1223, N.1226, L.1227, S.1231, L.1232, I.1235, L.1344, S.1345 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.249, A:I.253, A:I.619, A:I.623, A:L.1227, A:I.1235, A:L.1344 Hydrogen bonds: A:I.615, A:N.1226, A:N.1226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, J. et al., Conformational changes of a phosphatidylcholine flippase in lipid membranes. Cell Rep (2022)

Release Date

2022-03-23

Peptides

Phospholipid-transporting ATPase DNF1: A
Alkylphosphocholine resistance protein LEM3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Phospholipid-transporting ATPase DNF1

Alkylphosphocholine resistance protein LEM3

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